1 – Viruses Background, Classification and Principles
What is a virus
- Package of misinformation which replicates ONLY in the host
- Dependent on the host for energy metabolism, lipid biogenesis, and protein synthesis
- Produced de novo from pre-formed components
Important terms:
- Virion: the physical virus particle
- Capsid: protein shell surrounding viral nucleic acids
- Nucleocapsid: capsid + nucleic acid
- Envelope: lipid membrane that surrounds the capsid (only present on some, not all)
General scheme of virus replication cycle:
1. Attachment with specific interactions with host protein receptor
2. Penetration
3. Uncoating: release content
4. Replication: synthesis of viral mRNA, viral protein (for new capsids), viral nucleic acid
5. Assembly: capsids form around nucleic acid
6. Release: envelope (budding to form lipid viral membrane) and no envelope (kill the cell for
release)
Virus Diversity and Classification
There is a wide diversity of viruses based on genetic makeup, replication strategies, virion shape,
host specificity, disease, etc.
Baltimore classification (based on viral genome):
1. dsDNA: e.g. herpes
2. ssDNA
3. dsRNA
4. (+) ssRNA: directly translated by ribosome
5. (-) ssRNA: complement of (+) RNA, cannot be translated and thus have to encode their own RNA
polymerase (e.g. influenza, ebola)
6. Retrovirus: needs to RT RNA to DNA (e.g. HIV)
7. Gapped dsDNA
More classification based on physical characteristics:
- Symmetry of capsid: helical vs icosahedral
- Presence/absence of lipid membrane: enveloped vs naked
- Dimensions of virion and capsid: size and shape
, 2 – Virus Diagnostics
A good detection test should be:
- Fast
- Easy to do and interpret
- Financially beneficial
- Stable (storage)
- Sensitive (few false negatives)
- Specific (few false positives)
Direct vs Indirect Laboratory Diagnostics
Direct Indirect
Detection of? Detection techniques Detection of? Detection techniques
Subparticle of the Culture-based Immune response Antibody ELISA,
virus techniques (antibodies in agglutination test
Electron microscopy patient’s serum)
Whole microorganism
Viral proteins Antigen ELISA
Fluorescence
microscopy
Lateral flow assay
Genetic material PCR
Sequencing
Their products: toxins
1. Microscopy
- Not used in routine diagnostics
- Costly
- Only to visualize, not to identify
- Nurses/diagnostic technicians are not trained to use EM
2. Culture-based
- To detect a cytopathic effect (CPE)
which is the damage the virus has
done to the cells
- If the cell type is susceptible to viral
infection, non-infected cells
become infected and the cells die
(extreme type of CPE)
- Sample: urine, blood and feces
- Types of CPE: owl’s eye (fusion of
two neighboring cells), cell death
, - CPE can be used to quantify viruses: plaque assay and end point dilution
- Plaque assay: to measure how much virus is present in the sample prior to dilution but by
the time you know how much the virus is, the infection has already progressed so the
information you get is no longer useful
- In a petri dish, a mono-layer of cells are cultured → infect with diluted viral sample
→ observe cell death (plaques) → perform back calculation to count how much virus
was in the original sample
- Needs only a few viral particles otherwise the death rate is too fast to observe
- Agarose is used to ensure the virus to stay local and infect neighboring cells
- Using immunocompromised cells (lacking interferons) because they are susceptible to
infections
3. qPCR
- Taqman PCR is generally used: measure fluorescence
- The lower the CT value, the more RNA/DNA is present in the sample
- With PCR, you need some information regarding the virus first because you need to design a
primer
Culture based vs PCR
Culture based PCR
Advantages Detection of infectious High sensitivity
particles
Gives the chance to find the High specificity
unexpected: dealing with a
new disease
Relatively short time between
sample collection to result
Disadvantages More laborious Relatively expensive
Long waiting time from sample High sensitivity (What is the
collection to result point between being infectious
and having the remnants?)
Virus identification is often not Analysis is biased towards
possible expected viruses
4. Sequencing (NGS)
5. ELISA (enzyme linked immunosorbent assay)
- Antigen:
- Bind antibody to solid phase
- Add unknown antigen
- Detect bound antigen with labeled 2nd antibody
- Measure label
- Antibody:
- Bind antigen to solid phase
, - Add unknown antibody
- Detect bound antibody with labeled antibody
- Measure label
Antibody response to infection
- The initial response: IgM mediated, declines in a few weeks
- Isotype switching: IgM → IgG after a few weeks, detectable for many months/years after,
sometimes even lifelong
- Seroconversion: the development of a specific antibody response as a result of immunization
3 – Arboviruses: Virus Replication and Transmission
Arbo is not a family of viruses but it is a way of transmission → arthropod-borne (Insects,
crustacean, anything with the exoskeleton) primarily mosquitoes but also sandflies, gnats, and ticks.
Arboviruses are a major burden in subtropical countries in which the majority of the infections are
asymptomatic or result in mild, mostly generic symptoms (flu-like symptoms). These symptoms are
primarily caused by the activation of the immune system.
Arboviruses diseases can lead to many complications such as:
- Yellow fever: liver damage → yellow eye, the person turns yellow due to failure in bilirubin
metabolism
- West Nile virus: brain inflammation
- Chikungunya: fever and joint pain
- Dengue: internal bleeding → hemorrhagic fever → large bruises
- Zika: congenital Zika syndrome e.g. microcephaly (underdeveloped brain skull and brain.
Development in the unborn child (mother gets infected)
Virus tropism determines where the
virus goes, which kind of cells and
organs are infected and even what kind
of species get infected. Virus tropism is
determined by the presence of
susceptible cells.
Virus tropism alone cannot explain
different outcomes of virus infections:
in laboratory conditions, dengue and
Zika virus can infect similar cell types.
Zika virus
Zika can infect:
- Developing neurons in the brain: ZIKV can cross the blood-brain barrier
- Causes Guillain Barré Syndrome (GBS) and congenital Zika syndrome (CZS)
- GBS: the destruction of the myelin sheath (insulation) in the neurons
- CZS: microcephaly, muscular degeneration and craniofacial and musculoskeletal lesions
- Placenta: Infection of the fetal brain likely accounts for neuropathological features
- Eyes
What is a virus
- Package of misinformation which replicates ONLY in the host
- Dependent on the host for energy metabolism, lipid biogenesis, and protein synthesis
- Produced de novo from pre-formed components
Important terms:
- Virion: the physical virus particle
- Capsid: protein shell surrounding viral nucleic acids
- Nucleocapsid: capsid + nucleic acid
- Envelope: lipid membrane that surrounds the capsid (only present on some, not all)
General scheme of virus replication cycle:
1. Attachment with specific interactions with host protein receptor
2. Penetration
3. Uncoating: release content
4. Replication: synthesis of viral mRNA, viral protein (for new capsids), viral nucleic acid
5. Assembly: capsids form around nucleic acid
6. Release: envelope (budding to form lipid viral membrane) and no envelope (kill the cell for
release)
Virus Diversity and Classification
There is a wide diversity of viruses based on genetic makeup, replication strategies, virion shape,
host specificity, disease, etc.
Baltimore classification (based on viral genome):
1. dsDNA: e.g. herpes
2. ssDNA
3. dsRNA
4. (+) ssRNA: directly translated by ribosome
5. (-) ssRNA: complement of (+) RNA, cannot be translated and thus have to encode their own RNA
polymerase (e.g. influenza, ebola)
6. Retrovirus: needs to RT RNA to DNA (e.g. HIV)
7. Gapped dsDNA
More classification based on physical characteristics:
- Symmetry of capsid: helical vs icosahedral
- Presence/absence of lipid membrane: enveloped vs naked
- Dimensions of virion and capsid: size and shape
, 2 – Virus Diagnostics
A good detection test should be:
- Fast
- Easy to do and interpret
- Financially beneficial
- Stable (storage)
- Sensitive (few false negatives)
- Specific (few false positives)
Direct vs Indirect Laboratory Diagnostics
Direct Indirect
Detection of? Detection techniques Detection of? Detection techniques
Subparticle of the Culture-based Immune response Antibody ELISA,
virus techniques (antibodies in agglutination test
Electron microscopy patient’s serum)
Whole microorganism
Viral proteins Antigen ELISA
Fluorescence
microscopy
Lateral flow assay
Genetic material PCR
Sequencing
Their products: toxins
1. Microscopy
- Not used in routine diagnostics
- Costly
- Only to visualize, not to identify
- Nurses/diagnostic technicians are not trained to use EM
2. Culture-based
- To detect a cytopathic effect (CPE)
which is the damage the virus has
done to the cells
- If the cell type is susceptible to viral
infection, non-infected cells
become infected and the cells die
(extreme type of CPE)
- Sample: urine, blood and feces
- Types of CPE: owl’s eye (fusion of
two neighboring cells), cell death
, - CPE can be used to quantify viruses: plaque assay and end point dilution
- Plaque assay: to measure how much virus is present in the sample prior to dilution but by
the time you know how much the virus is, the infection has already progressed so the
information you get is no longer useful
- In a petri dish, a mono-layer of cells are cultured → infect with diluted viral sample
→ observe cell death (plaques) → perform back calculation to count how much virus
was in the original sample
- Needs only a few viral particles otherwise the death rate is too fast to observe
- Agarose is used to ensure the virus to stay local and infect neighboring cells
- Using immunocompromised cells (lacking interferons) because they are susceptible to
infections
3. qPCR
- Taqman PCR is generally used: measure fluorescence
- The lower the CT value, the more RNA/DNA is present in the sample
- With PCR, you need some information regarding the virus first because you need to design a
primer
Culture based vs PCR
Culture based PCR
Advantages Detection of infectious High sensitivity
particles
Gives the chance to find the High specificity
unexpected: dealing with a
new disease
Relatively short time between
sample collection to result
Disadvantages More laborious Relatively expensive
Long waiting time from sample High sensitivity (What is the
collection to result point between being infectious
and having the remnants?)
Virus identification is often not Analysis is biased towards
possible expected viruses
4. Sequencing (NGS)
5. ELISA (enzyme linked immunosorbent assay)
- Antigen:
- Bind antibody to solid phase
- Add unknown antigen
- Detect bound antigen with labeled 2nd antibody
- Measure label
- Antibody:
- Bind antigen to solid phase
, - Add unknown antibody
- Detect bound antibody with labeled antibody
- Measure label
Antibody response to infection
- The initial response: IgM mediated, declines in a few weeks
- Isotype switching: IgM → IgG after a few weeks, detectable for many months/years after,
sometimes even lifelong
- Seroconversion: the development of a specific antibody response as a result of immunization
3 – Arboviruses: Virus Replication and Transmission
Arbo is not a family of viruses but it is a way of transmission → arthropod-borne (Insects,
crustacean, anything with the exoskeleton) primarily mosquitoes but also sandflies, gnats, and ticks.
Arboviruses are a major burden in subtropical countries in which the majority of the infections are
asymptomatic or result in mild, mostly generic symptoms (flu-like symptoms). These symptoms are
primarily caused by the activation of the immune system.
Arboviruses diseases can lead to many complications such as:
- Yellow fever: liver damage → yellow eye, the person turns yellow due to failure in bilirubin
metabolism
- West Nile virus: brain inflammation
- Chikungunya: fever and joint pain
- Dengue: internal bleeding → hemorrhagic fever → large bruises
- Zika: congenital Zika syndrome e.g. microcephaly (underdeveloped brain skull and brain.
Development in the unborn child (mother gets infected)
Virus tropism determines where the
virus goes, which kind of cells and
organs are infected and even what kind
of species get infected. Virus tropism is
determined by the presence of
susceptible cells.
Virus tropism alone cannot explain
different outcomes of virus infections:
in laboratory conditions, dengue and
Zika virus can infect similar cell types.
Zika virus
Zika can infect:
- Developing neurons in the brain: ZIKV can cross the blood-brain barrier
- Causes Guillain Barré Syndrome (GBS) and congenital Zika syndrome (CZS)
- GBS: the destruction of the myelin sheath (insulation) in the neurons
- CZS: microcephaly, muscular degeneration and craniofacial and musculoskeletal lesions
- Placenta: Infection of the fetal brain likely accounts for neuropathological features
- Eyes
